Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq.

Journal article

Despite the many advantages of Caenorhabditis elegans, biochemical approaches to study tissue-specific gene expression in post-embryonic stages are challenging. Here, we report a novel experimental approach for efficient determination of tissue-specific transcriptomes involving the rapid release and purification of nuclei from major tissues of post-embryonic animals by fluorescence-activated nuclei sorting (FANS), followed by deep sequencing of linearly amplified 3'-end regions of transcripts (3'-end-seq). We employed these approaches to compile the transcriptome of the developed C. elegans intestine and used this to analyse tissue-specific cleavage and polyadenylation. In agreement with intestinal-specific gene expression, highly expressed genes have enriched GATA-elements in their promoter regions and their functional properties are associated with processes that are characteristic for the intestine. We systematically mapped pre-mRNA cleavage and polyadenylation sites, or polyA sites, including more than 3000 sites that have previously not been identified. The detailed analysis of the 3'-ends of the nuclear mRNA revealed widespread alternative polyA site use (APA) in intestinally expressed genes. Importantly, we found that intestinal polyA sites that undergo APA tend to have U-rich and/or A-rich upstream auxiliary elements that may contribute to the regulation of 3'-end formation in the intestine.

Authors: Haenni, S; Ji, Z; Hoque, M; Rust, N; Sharpe, H

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Nucleic acids research
• Volume: 40
• Issue: 13
• Pages: 6304-6318
• Publication date: 2012-07-01
• DOI: 10.1093/nar/gks282
• EISSN: 1362-4962
• ISSN: 0305-1048
• Language: English
• Keywords: Caenorhabditis elegans; Polyadenylation; Intestines; Sequence Analysis, RNA; Cell Fractionation; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Transcriptome; Cell Nucleus; Animals; Flow Cytometry